I've spent hours looking for a location for a second battery without making any modification and the only place I could find was somewhere on top of the bumper beam. I would be a tight squeeze for even a small battery.
What is the purpose of the second AGM battery again? IMO it seems overkill to have 3 separate batteries. I understand wanting to have an 100% isolated system but it seems like a lot of work for very little to no benefit. Most of the accessories that you would run off the second underhood battery could either be run off the starting battery or house battery, depending on the usage. Anything major loads like a winch or compressor would be running only with the engine running so the alternator is doing most of the work.
I have my GX setup with a separate Lithium in the cargo area. My reasoning for doing that is most of the constant loads like fridge, inverter, air compressor, that run off the house battery are in the cargo area, so it was easier to run on set of heavy gauge wires for the battery rather than multiple wires for the accessories. I have all add on accessories running off a separate fuse/relay box near the brake booster, so the stock wiring stays untouched. The downside of this is you don't have the ability to self jumpstart easily, but with most of the load running off the lithium battery the chances of killing the start battery go way down. Plus I always have a lithium jumpstarter as a backup, between those two items it makes the need to self jumpstart almost non-existent.
